General Sarath Fonseka said Gotabhaya Rajapakse -- the brother of the current president -- instructed field commanders not to take prisoners in the days before the Tamil Tiger separatists were defeated in May.
"Gotabhaya Rajapakse spoke directly with (commander) Shavendra Silva and told him not to accommodate any surrendering LTTE leaders and that they must all be killed," Fonseka told reporters at a meeting of opposition parties.
Fonseka said he was away in China and was unaware that Rajapakse was giving direct orders to officers in the field during the final stages of battle against the Tigers, officially known as the Liberation Tigers of Tamil Eelam.
He said he only learnt after the war that senior Tiger rebels had used foreign mediators to organise a plan in which they would carry white flags and give themselves up.
Fonseka led the army's successful offensive to finally crush the LTTE and end the island's decades-long ethnic conflict, but he later fell out with President Mahi